Your websites structure is like the base of a house – it is the building blocks of the website. So you should consider how the individual subpages are linked to each other and how does these lead to a navigation- and sitestructure of your website. For example should your primary navigation be via search or hierarchical “fold out” or something third like a top bar navigation. It is also particularly important with regards to crawlers so they can find all your subpages, in particular when your site has a large number of subpages this becomes increasingly important. XML sitemaps can be created and can be submitted to Google, Bing, Yahoo and other search engines to help them crawl your website.
Even though webpages uses many different and creative structures and designs, some common and accepted standard structures have been adapted. Following the web style guide (3rd edision) most websites incorporate some or all these basic components: